Multiple sequence alignment - TraesCS1B01G407900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G407900 chr1B 100.000 2508 0 0 1 2508 635001468 634998961 0.000000e+00 4632.0
1 TraesCS1B01G407900 chr1B 96.707 1822 55 4 689 2508 634785294 634783476 0.000000e+00 3027.0
2 TraesCS1B01G407900 chr1B 90.781 1703 118 15 783 2467 635140466 635138785 0.000000e+00 2239.0
3 TraesCS1B01G407900 chr1B 90.851 1246 79 12 783 2023 634866523 634865308 0.000000e+00 1637.0
4 TraesCS1B01G407900 chr1B 90.770 1246 80 12 783 2023 634935077 634933862 0.000000e+00 1631.0
5 TraesCS1B01G407900 chr1B 86.292 445 51 2 11 445 14249184 14249628 2.260000e-130 475.0
6 TraesCS1B01G407900 chr1B 79.617 574 72 26 1754 2322 635087902 635087369 1.100000e-98 370.0
7 TraesCS1B01G407900 chr1B 88.889 126 8 4 598 719 635141622 635141499 1.550000e-32 150.0
8 TraesCS1B01G407900 chr1B 86.111 72 8 1 715 784 634866929 634866858 2.680000e-10 76.8
9 TraesCS1B01G407900 chr1B 86.111 72 8 1 715 784 634935483 634935412 2.680000e-10 76.8
10 TraesCS1B01G407900 chr1B 86.111 72 8 1 715 784 635140870 635140799 2.680000e-10 76.8
11 TraesCS1B01G407900 chr1B 82.895 76 11 2 514 588 487924652 487924726 1.610000e-07 67.6
12 TraesCS1B01G407900 chr1B 76.852 108 20 5 511 615 389315655 389315760 3.490000e-04 56.5
13 TraesCS1B01G407900 chr1B 76.923 104 21 3 511 613 496511371 496511472 3.490000e-04 56.5
14 TraesCS1B01G407900 chr1D 91.727 1922 117 21 605 2508 461788057 461786160 0.000000e+00 2630.0
15 TraesCS1B01G407900 chr1D 90.202 1235 82 11 790 2022 461823132 461821935 0.000000e+00 1574.0
16 TraesCS1B01G407900 chr1D 81.431 657 76 26 1754 2406 461751790 461751176 1.730000e-136 496.0
17 TraesCS1B01G407900 chr1D 85.117 383 43 11 75 444 468845065 468844684 1.820000e-101 379.0
18 TraesCS1B01G407900 chr1D 86.508 126 12 4 598 719 461824342 461824218 1.570000e-27 134.0
19 TraesCS1B01G407900 chr6B 90.519 1656 125 13 858 2508 661863222 661861594 0.000000e+00 2159.0
20 TraesCS1B01G407900 chr6B 83.465 381 47 6 64 444 572492750 572493114 8.590000e-90 340.0
21 TraesCS1B01G407900 chrUn 90.824 1177 73 12 783 1954 350030104 350031250 0.000000e+00 1543.0
22 TraesCS1B01G407900 chrUn 86.111 72 8 1 715 784 350029698 350029769 2.680000e-10 76.8
23 TraesCS1B01G407900 chr1A 89.704 913 65 8 790 1700 553466062 553465177 0.000000e+00 1138.0
24 TraesCS1B01G407900 chr1A 87.588 709 48 5 779 1461 553135335 553136029 0.000000e+00 785.0
25 TraesCS1B01G407900 chr1A 80.211 662 81 26 1754 2406 553046336 553045716 3.800000e-123 451.0
26 TraesCS1B01G407900 chr1A 91.212 330 27 2 1693 2022 553464877 553464550 4.920000e-122 448.0
27 TraesCS1B01G407900 chr1A 92.258 310 20 4 1575 1884 553068399 553068094 1.070000e-118 436.0
28 TraesCS1B01G407900 chr1A 82.579 442 57 11 21 444 30540268 30540707 3.050000e-99 372.0
29 TraesCS1B01G407900 chr1A 80.963 457 64 11 11 445 516853008 516852553 8.590000e-90 340.0
30 TraesCS1B01G407900 chr1A 91.787 207 8 4 442 645 553133888 553134088 1.900000e-71 279.0
31 TraesCS1B01G407900 chr1A 85.938 64 7 2 511 573 544448670 544448732 1.610000e-07 67.6
32 TraesCS1B01G407900 chr3D 86.253 451 45 1 11 444 584598068 584597618 8.120000e-130 473.0
33 TraesCS1B01G407900 chr3B 85.809 451 47 2 11 444 796283718 796283268 1.760000e-126 462.0
34 TraesCS1B01G407900 chr3B 85.287 401 40 9 63 445 735108477 735108876 1.810000e-106 396.0
35 TraesCS1B01G407900 chr4A 85.078 449 45 10 18 444 651364148 651364596 2.960000e-119 438.0
36 TraesCS1B01G407900 chr5D 83.486 436 60 5 11 445 440201715 440201291 1.810000e-106 396.0
37 TraesCS1B01G407900 chr7A 80.306 457 67 11 11 445 724959258 724959713 8.650000e-85 324.0
38 TraesCS1B01G407900 chr7A 79.412 102 15 6 515 612 157954994 157954895 1.610000e-07 67.6
39 TraesCS1B01G407900 chr7A 78.302 106 17 6 511 612 157971431 157971328 2.080000e-06 63.9
40 TraesCS1B01G407900 chr2D 82.857 105 11 6 511 612 625538397 625538497 1.240000e-13 87.9
41 TraesCS1B01G407900 chr5A 77.670 103 21 2 511 612 365849266 365849165 7.490000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G407900 chr1B 634998961 635001468 2507 True 4632.000000 4632 100.000000 1 2508 1 chr1B.!!$R2 2507
1 TraesCS1B01G407900 chr1B 634783476 634785294 1818 True 3027.000000 3027 96.707000 689 2508 1 chr1B.!!$R1 1819
2 TraesCS1B01G407900 chr1B 634865308 634866929 1621 True 856.900000 1637 88.481000 715 2023 2 chr1B.!!$R4 1308
3 TraesCS1B01G407900 chr1B 634933862 634935483 1621 True 853.900000 1631 88.440500 715 2023 2 chr1B.!!$R5 1308
4 TraesCS1B01G407900 chr1B 635138785 635141622 2837 True 821.933333 2239 88.593667 598 2467 3 chr1B.!!$R6 1869
5 TraesCS1B01G407900 chr1B 635087369 635087902 533 True 370.000000 370 79.617000 1754 2322 1 chr1B.!!$R3 568
6 TraesCS1B01G407900 chr1D 461786160 461788057 1897 True 2630.000000 2630 91.727000 605 2508 1 chr1D.!!$R2 1903
7 TraesCS1B01G407900 chr1D 461821935 461824342 2407 True 854.000000 1574 88.355000 598 2022 2 chr1D.!!$R4 1424
8 TraesCS1B01G407900 chr1D 461751176 461751790 614 True 496.000000 496 81.431000 1754 2406 1 chr1D.!!$R1 652
9 TraesCS1B01G407900 chr6B 661861594 661863222 1628 True 2159.000000 2159 90.519000 858 2508 1 chr6B.!!$R1 1650
10 TraesCS1B01G407900 chrUn 350029698 350031250 1552 False 809.900000 1543 88.467500 715 1954 2 chrUn.!!$F1 1239
11 TraesCS1B01G407900 chr1A 553464550 553466062 1512 True 793.000000 1138 90.458000 790 2022 2 chr1A.!!$R4 1232
12 TraesCS1B01G407900 chr1A 553133888 553136029 2141 False 532.000000 785 89.687500 442 1461 2 chr1A.!!$F3 1019
13 TraesCS1B01G407900 chr1A 553045716 553046336 620 True 451.000000 451 80.211000 1754 2406 1 chr1A.!!$R2 652

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
149 150 0.029834 GGATCAATGACGTGGCATGC 59.97 55.0 9.9 9.9 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 4394 1.069227 GTTGAATCTCCACAACGTGCC 60.069 52.381 0.0 0.0 37.29 5.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.408835 GGCAATCCGACGGCATTG 59.591 61.111 23.47 23.47 33.77 2.82
22 23 2.278142 GCAATCCGACGGCATTGC 60.278 61.111 30.30 30.30 45.97 3.56
23 24 2.408835 CAATCCGACGGCATTGCC 59.591 61.111 18.10 18.10 46.75 4.52
45 46 2.506065 GGCATAGAGACGACAGGGT 58.494 57.895 0.00 0.00 0.00 4.34
46 47 0.824759 GGCATAGAGACGACAGGGTT 59.175 55.000 0.00 0.00 0.00 4.11
47 48 1.207329 GGCATAGAGACGACAGGGTTT 59.793 52.381 0.00 0.00 0.00 3.27
48 49 2.429610 GGCATAGAGACGACAGGGTTTA 59.570 50.000 0.00 0.00 0.00 2.01
49 50 3.491104 GGCATAGAGACGACAGGGTTTAG 60.491 52.174 0.00 0.00 0.00 1.85
50 51 3.491104 GCATAGAGACGACAGGGTTTAGG 60.491 52.174 0.00 0.00 0.00 2.69
51 52 0.896226 AGAGACGACAGGGTTTAGGC 59.104 55.000 0.00 0.00 0.00 3.93
52 53 0.458025 GAGACGACAGGGTTTAGGCG 60.458 60.000 0.00 0.00 0.00 5.52
53 54 1.447314 GACGACAGGGTTTAGGCGG 60.447 63.158 0.00 0.00 0.00 6.13
54 55 2.125269 CGACAGGGTTTAGGCGGG 60.125 66.667 0.00 0.00 0.00 6.13
55 56 2.437895 GACAGGGTTTAGGCGGGC 60.438 66.667 0.00 0.00 0.00 6.13
56 57 4.404098 ACAGGGTTTAGGCGGGCG 62.404 66.667 0.00 0.00 0.00 6.13
57 58 4.090588 CAGGGTTTAGGCGGGCGA 62.091 66.667 0.00 0.00 0.00 5.54
58 59 4.091939 AGGGTTTAGGCGGGCGAC 62.092 66.667 0.00 0.00 0.00 5.19
60 61 4.747529 GGTTTAGGCGGGCGACGT 62.748 66.667 0.00 0.00 46.52 4.34
61 62 3.484547 GTTTAGGCGGGCGACGTG 61.485 66.667 0.00 0.00 46.52 4.49
82 83 4.498520 CGGATCGCTGACGTGGCT 62.499 66.667 0.00 0.00 41.18 4.75
83 84 2.887568 GGATCGCTGACGTGGCTG 60.888 66.667 0.00 0.00 41.18 4.85
84 85 2.887568 GATCGCTGACGTGGCTGG 60.888 66.667 0.00 0.00 41.18 4.85
85 86 3.649277 GATCGCTGACGTGGCTGGT 62.649 63.158 0.00 0.00 41.18 4.00
86 87 2.279502 GATCGCTGACGTGGCTGGTA 62.280 60.000 0.00 0.00 41.18 3.25
87 88 1.676678 ATCGCTGACGTGGCTGGTAT 61.677 55.000 0.00 0.00 41.18 2.73
88 89 2.167219 CGCTGACGTGGCTGGTATG 61.167 63.158 0.00 0.00 33.53 2.39
89 90 2.464459 GCTGACGTGGCTGGTATGC 61.464 63.158 0.00 0.00 0.00 3.14
110 111 2.100216 CGGCAGCCGTTTGCATAC 59.900 61.111 26.69 0.00 45.86 2.39
111 112 2.100216 GGCAGCCGTTTGCATACG 59.900 61.111 20.86 20.86 45.86 3.06
112 113 2.686816 GGCAGCCGTTTGCATACGT 61.687 57.895 24.61 7.82 45.86 3.57
113 114 1.511887 GCAGCCGTTTGCATACGTG 60.512 57.895 24.61 18.75 44.83 4.49
114 115 1.866237 CAGCCGTTTGCATACGTGT 59.134 52.632 24.61 11.18 44.83 4.49
115 116 0.237235 CAGCCGTTTGCATACGTGTT 59.763 50.000 24.61 13.34 44.83 3.32
116 117 0.237235 AGCCGTTTGCATACGTGTTG 59.763 50.000 24.61 12.68 44.83 3.33
117 118 0.727793 GCCGTTTGCATACGTGTTGG 60.728 55.000 24.61 12.36 39.81 3.77
118 119 0.869068 CCGTTTGCATACGTGTTGGA 59.131 50.000 24.61 0.00 39.81 3.53
119 120 1.399215 CCGTTTGCATACGTGTTGGAC 60.399 52.381 24.61 0.00 39.81 4.02
138 139 4.596180 GTGCGCCGCGGATCAATG 62.596 66.667 33.48 11.45 0.00 2.82
139 140 4.828925 TGCGCCGCGGATCAATGA 62.829 61.111 33.48 0.65 0.00 2.57
140 141 4.299316 GCGCCGCGGATCAATGAC 62.299 66.667 33.48 7.28 0.00 3.06
141 142 3.988385 CGCCGCGGATCAATGACG 61.988 66.667 33.48 16.81 0.00 4.35
142 143 2.890474 GCCGCGGATCAATGACGT 60.890 61.111 33.48 0.00 0.00 4.34
143 144 3.005898 CCGCGGATCAATGACGTG 58.994 61.111 24.07 0.64 37.81 4.49
144 145 3.005898 CGCGGATCAATGACGTGG 58.994 61.111 0.00 0.00 34.78 4.94
145 146 2.709475 GCGGATCAATGACGTGGC 59.291 61.111 0.00 0.00 0.00 5.01
146 147 2.106074 GCGGATCAATGACGTGGCA 61.106 57.895 0.00 0.00 0.00 4.92
147 148 1.439353 GCGGATCAATGACGTGGCAT 61.439 55.000 0.00 0.00 0.00 4.40
148 149 0.305617 CGGATCAATGACGTGGCATG 59.694 55.000 4.87 4.87 0.00 4.06
149 150 0.029834 GGATCAATGACGTGGCATGC 59.970 55.000 9.90 9.90 0.00 4.06
150 151 0.316442 GATCAATGACGTGGCATGCG 60.316 55.000 12.44 0.54 0.00 4.73
151 152 1.717791 ATCAATGACGTGGCATGCGG 61.718 55.000 12.44 6.03 0.00 5.69
152 153 2.046411 AATGACGTGGCATGCGGA 60.046 55.556 12.44 0.00 0.00 5.54
153 154 2.108514 AATGACGTGGCATGCGGAG 61.109 57.895 12.44 7.48 0.00 4.63
154 155 2.520465 AATGACGTGGCATGCGGAGA 62.520 55.000 12.44 0.00 0.00 3.71
155 156 2.202932 GACGTGGCATGCGGAGAT 60.203 61.111 12.44 0.00 0.00 2.75
156 157 1.067416 GACGTGGCATGCGGAGATA 59.933 57.895 12.44 0.00 0.00 1.98
157 158 0.319900 GACGTGGCATGCGGAGATAT 60.320 55.000 12.44 0.00 0.00 1.63
158 159 0.601046 ACGTGGCATGCGGAGATATG 60.601 55.000 12.44 1.94 0.00 1.78
159 160 1.871772 GTGGCATGCGGAGATATGC 59.128 57.895 12.44 0.00 44.78 3.14
183 184 4.586235 CCGCCCATCCCCACCATC 62.586 72.222 0.00 0.00 0.00 3.51
184 185 4.935495 CGCCCATCCCCACCATCG 62.935 72.222 0.00 0.00 0.00 3.84
185 186 4.586235 GCCCATCCCCACCATCGG 62.586 72.222 0.00 0.00 0.00 4.18
186 187 4.586235 CCCATCCCCACCATCGGC 62.586 72.222 0.00 0.00 0.00 5.54
187 188 3.807839 CCATCCCCACCATCGGCA 61.808 66.667 0.00 0.00 0.00 5.69
188 189 2.517414 CATCCCCACCATCGGCAT 59.483 61.111 0.00 0.00 0.00 4.40
189 190 1.760527 CATCCCCACCATCGGCATA 59.239 57.895 0.00 0.00 0.00 3.14
190 191 0.321919 CATCCCCACCATCGGCATAG 60.322 60.000 0.00 0.00 0.00 2.23
191 192 0.473694 ATCCCCACCATCGGCATAGA 60.474 55.000 0.00 0.00 0.00 1.98
192 193 0.473694 TCCCCACCATCGGCATAGAT 60.474 55.000 0.00 0.00 0.00 1.98
193 194 0.401738 CCCCACCATCGGCATAGATT 59.598 55.000 0.00 0.00 0.00 2.40
194 195 1.202927 CCCCACCATCGGCATAGATTT 60.203 52.381 0.00 0.00 0.00 2.17
195 196 1.881973 CCCACCATCGGCATAGATTTG 59.118 52.381 0.00 0.00 0.00 2.32
196 197 2.487086 CCCACCATCGGCATAGATTTGA 60.487 50.000 0.00 0.00 0.00 2.69
197 198 2.549754 CCACCATCGGCATAGATTTGAC 59.450 50.000 0.00 0.00 0.00 3.18
198 199 3.205338 CACCATCGGCATAGATTTGACA 58.795 45.455 0.00 0.00 0.00 3.58
199 200 3.627123 CACCATCGGCATAGATTTGACAA 59.373 43.478 0.00 0.00 0.00 3.18
200 201 4.276678 CACCATCGGCATAGATTTGACAAT 59.723 41.667 0.00 0.00 0.00 2.71
201 202 4.276678 ACCATCGGCATAGATTTGACAATG 59.723 41.667 0.00 0.00 0.00 2.82
202 203 4.276678 CCATCGGCATAGATTTGACAATGT 59.723 41.667 0.00 0.00 0.00 2.71
203 204 5.221106 CCATCGGCATAGATTTGACAATGTT 60.221 40.000 0.00 0.00 0.00 2.71
204 205 6.017192 CCATCGGCATAGATTTGACAATGTTA 60.017 38.462 0.00 0.00 0.00 2.41
205 206 6.603237 TCGGCATAGATTTGACAATGTTAG 57.397 37.500 0.00 0.00 0.00 2.34
206 207 5.007626 TCGGCATAGATTTGACAATGTTAGC 59.992 40.000 0.00 0.00 0.00 3.09
207 208 5.523369 GGCATAGATTTGACAATGTTAGCC 58.477 41.667 0.00 0.00 31.55 3.93
208 209 5.207768 GCATAGATTTGACAATGTTAGCCG 58.792 41.667 0.00 0.00 0.00 5.52
209 210 5.007626 GCATAGATTTGACAATGTTAGCCGA 59.992 40.000 0.00 0.00 0.00 5.54
210 211 6.293626 GCATAGATTTGACAATGTTAGCCGAT 60.294 38.462 0.00 0.00 0.00 4.18
211 212 5.490139 AGATTTGACAATGTTAGCCGATG 57.510 39.130 0.00 0.00 0.00 3.84
212 213 4.336433 AGATTTGACAATGTTAGCCGATGG 59.664 41.667 0.00 0.00 0.00 3.51
213 214 2.779755 TGACAATGTTAGCCGATGGT 57.220 45.000 0.00 0.00 0.00 3.55
214 215 2.627945 TGACAATGTTAGCCGATGGTC 58.372 47.619 0.00 0.00 0.00 4.02
215 216 2.027653 TGACAATGTTAGCCGATGGTCA 60.028 45.455 0.00 0.00 0.00 4.02
216 217 2.351726 GACAATGTTAGCCGATGGTCAC 59.648 50.000 0.00 0.00 0.00 3.67
217 218 1.327460 CAATGTTAGCCGATGGTCACG 59.673 52.381 0.00 0.00 0.00 4.35
223 224 4.467084 CCGATGGTCACGGGTGGG 62.467 72.222 0.00 0.00 45.65 4.61
224 225 3.702048 CGATGGTCACGGGTGGGT 61.702 66.667 0.00 0.00 0.00 4.51
225 226 2.754375 GATGGTCACGGGTGGGTT 59.246 61.111 0.00 0.00 0.00 4.11
226 227 1.376812 GATGGTCACGGGTGGGTTC 60.377 63.158 0.00 0.00 0.00 3.62
227 228 2.119484 GATGGTCACGGGTGGGTTCA 62.119 60.000 0.00 0.00 0.00 3.18
228 229 2.281276 GGTCACGGGTGGGTTCAC 60.281 66.667 0.00 0.00 42.91 3.18
243 244 4.090588 CACCGGGCCCACGTGTAT 62.091 66.667 24.92 0.00 0.00 2.29
244 245 4.090588 ACCGGGCCCACGTGTATG 62.091 66.667 24.92 1.64 0.00 2.39
248 249 4.460683 GGCCCACGTGTATGCCGA 62.461 66.667 20.62 0.00 33.59 5.54
249 250 3.192922 GCCCACGTGTATGCCGAC 61.193 66.667 15.65 0.00 0.00 4.79
250 251 2.883730 CCCACGTGTATGCCGACG 60.884 66.667 15.65 0.00 41.41 5.12
251 252 2.179767 CCACGTGTATGCCGACGA 59.820 61.111 15.65 0.00 38.94 4.20
252 253 2.156446 CCACGTGTATGCCGACGAC 61.156 63.158 15.65 0.00 38.94 4.34
253 254 1.154093 CACGTGTATGCCGACGACT 60.154 57.895 7.58 0.00 38.94 4.18
254 255 0.097499 CACGTGTATGCCGACGACTA 59.903 55.000 7.58 0.00 38.94 2.59
255 256 0.376152 ACGTGTATGCCGACGACTAG 59.624 55.000 0.00 0.00 38.94 2.57
256 257 0.376152 CGTGTATGCCGACGACTAGT 59.624 55.000 0.00 0.00 37.81 2.57
257 258 1.202110 CGTGTATGCCGACGACTAGTT 60.202 52.381 0.00 0.00 37.81 2.24
258 259 2.730090 CGTGTATGCCGACGACTAGTTT 60.730 50.000 0.00 0.00 37.81 2.66
259 260 3.485711 CGTGTATGCCGACGACTAGTTTA 60.486 47.826 0.00 0.00 37.81 2.01
260 261 4.604976 GTGTATGCCGACGACTAGTTTAT 58.395 43.478 0.00 0.00 0.00 1.40
261 262 4.440103 GTGTATGCCGACGACTAGTTTATG 59.560 45.833 0.00 0.00 0.00 1.90
262 263 1.917273 TGCCGACGACTAGTTTATGC 58.083 50.000 0.00 0.00 0.00 3.14
263 264 1.206523 GCCGACGACTAGTTTATGCC 58.793 55.000 0.00 0.00 0.00 4.40
264 265 1.474017 CCGACGACTAGTTTATGCCG 58.526 55.000 0.00 0.00 0.00 5.69
265 266 1.064505 CCGACGACTAGTTTATGCCGA 59.935 52.381 0.00 0.00 0.00 5.54
266 267 2.107178 CGACGACTAGTTTATGCCGAC 58.893 52.381 0.00 0.00 0.00 4.79
267 268 2.107178 GACGACTAGTTTATGCCGACG 58.893 52.381 0.00 0.00 0.00 5.12
268 269 1.202222 ACGACTAGTTTATGCCGACGG 60.202 52.381 10.29 10.29 0.00 4.79
288 289 2.355837 GCTGTCGGCGTGTTCTCA 60.356 61.111 6.85 0.00 0.00 3.27
289 290 2.375766 GCTGTCGGCGTGTTCTCAG 61.376 63.158 6.85 8.39 0.00 3.35
290 291 2.355837 TGTCGGCGTGTTCTCAGC 60.356 61.111 6.85 0.00 0.00 4.26
291 292 2.049063 GTCGGCGTGTTCTCAGCT 60.049 61.111 6.85 0.00 0.00 4.24
292 293 1.211969 GTCGGCGTGTTCTCAGCTA 59.788 57.895 6.85 0.00 0.00 3.32
293 294 0.798771 GTCGGCGTGTTCTCAGCTAG 60.799 60.000 6.85 0.00 0.00 3.42
294 295 1.517257 CGGCGTGTTCTCAGCTAGG 60.517 63.158 0.00 0.00 0.00 3.02
295 296 1.811679 GGCGTGTTCTCAGCTAGGC 60.812 63.158 0.00 0.00 0.00 3.93
296 297 1.811679 GCGTGTTCTCAGCTAGGCC 60.812 63.158 0.00 0.00 0.00 5.19
297 298 1.517257 CGTGTTCTCAGCTAGGCCG 60.517 63.158 0.00 0.00 0.00 6.13
298 299 1.153549 GTGTTCTCAGCTAGGCCGG 60.154 63.158 0.00 0.00 0.00 6.13
299 300 2.202946 GTTCTCAGCTAGGCCGGC 60.203 66.667 21.18 21.18 0.00 6.13
300 301 3.838271 TTCTCAGCTAGGCCGGCG 61.838 66.667 22.54 8.08 34.52 6.46
311 312 2.102161 GCCGGCGGCTATTTTGTG 59.898 61.111 41.44 5.82 46.69 3.33
312 313 2.102161 CCGGCGGCTATTTTGTGC 59.898 61.111 15.42 0.00 0.00 4.57
313 314 2.102161 CGGCGGCTATTTTGTGCC 59.898 61.111 7.61 0.00 45.25 5.01
318 319 1.427819 GGCTATTTTGTGCCGACGG 59.572 57.895 10.29 10.29 39.71 4.79
319 320 1.303091 GGCTATTTTGTGCCGACGGT 61.303 55.000 16.73 0.00 39.71 4.83
320 321 0.519961 GCTATTTTGTGCCGACGGTT 59.480 50.000 16.73 0.00 0.00 4.44
321 322 1.727857 GCTATTTTGTGCCGACGGTTG 60.728 52.381 16.73 0.00 0.00 3.77
322 323 0.238817 TATTTTGTGCCGACGGTTGC 59.761 50.000 16.73 6.64 0.00 4.17
323 324 2.414840 ATTTTGTGCCGACGGTTGCC 62.415 55.000 16.73 0.00 0.00 4.52
345 346 1.740905 GGCTTAGACCGGAGTAGCC 59.259 63.158 19.95 19.95 43.96 3.93
346 347 1.740905 GCTTAGACCGGAGTAGCCC 59.259 63.158 9.46 0.00 0.00 5.19
361 362 4.838152 CCCGACGGCCAGGATGTG 62.838 72.222 8.86 0.00 0.00 3.21
369 370 2.821366 CCAGGATGTGGCTGTCGC 60.821 66.667 0.00 0.00 40.39 5.19
379 380 4.521075 GCTGTCGCCATAGCTCAA 57.479 55.556 0.00 0.00 36.99 3.02
380 381 2.997899 GCTGTCGCCATAGCTCAAT 58.002 52.632 0.00 0.00 36.99 2.57
381 382 0.864455 GCTGTCGCCATAGCTCAATC 59.136 55.000 0.00 0.00 36.99 2.67
382 383 1.539929 GCTGTCGCCATAGCTCAATCT 60.540 52.381 0.00 0.00 36.99 2.40
383 384 2.288457 GCTGTCGCCATAGCTCAATCTA 60.288 50.000 0.00 0.00 36.99 1.98
384 385 3.573598 CTGTCGCCATAGCTCAATCTAG 58.426 50.000 0.00 0.00 36.60 2.43
385 386 3.222603 TGTCGCCATAGCTCAATCTAGA 58.777 45.455 0.00 0.00 36.60 2.43
386 387 3.004839 TGTCGCCATAGCTCAATCTAGAC 59.995 47.826 0.00 0.00 36.60 2.59
387 388 2.558795 TCGCCATAGCTCAATCTAGACC 59.441 50.000 0.00 0.00 36.60 3.85
388 389 2.669670 CGCCATAGCTCAATCTAGACCG 60.670 54.545 0.00 0.00 36.60 4.79
389 390 2.558795 GCCATAGCTCAATCTAGACCGA 59.441 50.000 0.00 0.00 35.50 4.69
390 391 3.612955 GCCATAGCTCAATCTAGACCGAC 60.613 52.174 0.00 0.00 35.50 4.79
391 392 3.365465 CCATAGCTCAATCTAGACCGACG 60.365 52.174 0.00 0.00 0.00 5.12
392 393 1.025812 AGCTCAATCTAGACCGACGG 58.974 55.000 13.61 13.61 0.00 4.79
393 394 0.595310 GCTCAATCTAGACCGACGGC 60.595 60.000 15.39 7.02 0.00 5.68
394 395 0.317103 CTCAATCTAGACCGACGGCG 60.317 60.000 15.39 1.94 37.24 6.46
409 410 3.737172 GCGGCCGTCAGCATTGTT 61.737 61.111 28.70 0.00 46.50 2.83
410 411 2.953821 CGGCCGTCAGCATTGTTT 59.046 55.556 19.50 0.00 46.50 2.83
411 412 1.285641 CGGCCGTCAGCATTGTTTT 59.714 52.632 19.50 0.00 46.50 2.43
412 413 1.003262 CGGCCGTCAGCATTGTTTTG 61.003 55.000 19.50 0.00 46.50 2.44
413 414 0.667184 GGCCGTCAGCATTGTTTTGG 60.667 55.000 0.00 0.00 46.50 3.28
414 415 1.284297 GCCGTCAGCATTGTTTTGGC 61.284 55.000 0.00 0.00 42.97 4.52
415 416 0.667184 CCGTCAGCATTGTTTTGGCC 60.667 55.000 0.00 0.00 0.00 5.36
416 417 1.003262 CGTCAGCATTGTTTTGGCCG 61.003 55.000 0.00 0.00 0.00 6.13
417 418 0.031994 GTCAGCATTGTTTTGGCCGT 59.968 50.000 0.00 0.00 0.00 5.68
418 419 0.313672 TCAGCATTGTTTTGGCCGTC 59.686 50.000 0.00 0.00 0.00 4.79
419 420 1.003262 CAGCATTGTTTTGGCCGTCG 61.003 55.000 0.00 0.00 0.00 5.12
420 421 1.732683 GCATTGTTTTGGCCGTCGG 60.733 57.895 6.99 6.99 0.00 4.79
421 422 1.080839 CATTGTTTTGGCCGTCGGG 60.081 57.895 14.38 0.00 0.00 5.14
422 423 2.272447 ATTGTTTTGGCCGTCGGGG 61.272 57.895 14.38 0.00 39.58 5.73
423 424 2.987355 ATTGTTTTGGCCGTCGGGGT 62.987 55.000 14.38 0.00 38.44 4.95
424 425 2.032376 GTTTTGGCCGTCGGGGTA 59.968 61.111 14.38 0.00 38.44 3.69
425 426 2.036571 GTTTTGGCCGTCGGGGTAG 61.037 63.158 14.38 0.00 38.44 3.18
426 427 3.256824 TTTTGGCCGTCGGGGTAGG 62.257 63.158 14.38 0.00 38.44 3.18
427 428 4.700448 TTGGCCGTCGGGGTAGGA 62.700 66.667 14.38 0.00 38.44 2.94
430 431 3.525545 GCCGTCGGGGTAGGACTC 61.526 72.222 14.38 0.00 38.44 3.36
431 432 2.274760 CCGTCGGGGTAGGACTCT 59.725 66.667 2.34 0.00 32.24 3.24
432 433 1.379576 CCGTCGGGGTAGGACTCTT 60.380 63.158 2.34 0.00 32.24 2.85
433 434 0.969409 CCGTCGGGGTAGGACTCTTT 60.969 60.000 2.34 0.00 32.24 2.52
434 435 0.893447 CGTCGGGGTAGGACTCTTTT 59.107 55.000 0.00 0.00 32.24 2.27
435 436 1.135170 CGTCGGGGTAGGACTCTTTTC 60.135 57.143 0.00 0.00 32.24 2.29
436 437 2.177734 GTCGGGGTAGGACTCTTTTCT 58.822 52.381 0.00 0.00 0.00 2.52
437 438 2.094130 GTCGGGGTAGGACTCTTTTCTG 60.094 54.545 0.00 0.00 0.00 3.02
438 439 1.207329 CGGGGTAGGACTCTTTTCTGG 59.793 57.143 0.00 0.00 0.00 3.86
439 440 2.267192 GGGGTAGGACTCTTTTCTGGT 58.733 52.381 0.00 0.00 0.00 4.00
440 441 3.447950 GGGGTAGGACTCTTTTCTGGTA 58.552 50.000 0.00 0.00 0.00 3.25
441 442 3.451540 GGGGTAGGACTCTTTTCTGGTAG 59.548 52.174 0.00 0.00 0.00 3.18
442 443 4.095211 GGGTAGGACTCTTTTCTGGTAGT 58.905 47.826 0.00 0.00 0.00 2.73
443 444 4.081586 GGGTAGGACTCTTTTCTGGTAGTG 60.082 50.000 0.00 0.00 0.00 2.74
444 445 4.081586 GGTAGGACTCTTTTCTGGTAGTGG 60.082 50.000 0.00 0.00 0.00 4.00
445 446 2.907042 AGGACTCTTTTCTGGTAGTGGG 59.093 50.000 0.00 0.00 0.00 4.61
446 447 2.615747 GGACTCTTTTCTGGTAGTGGGC 60.616 54.545 0.00 0.00 0.00 5.36
447 448 1.002087 ACTCTTTTCTGGTAGTGGGCG 59.998 52.381 0.00 0.00 0.00 6.13
554 555 2.094545 GGGCAATCCTCACAACATGAAC 60.095 50.000 0.00 0.00 36.69 3.18
594 597 9.474313 ACATTATTACCCATCAATAAAGTGTGT 57.526 29.630 0.00 0.00 31.88 3.72
597 600 7.630242 ATTACCCATCAATAAAGTGTGTGAG 57.370 36.000 0.00 0.00 0.00 3.51
598 601 5.241403 ACCCATCAATAAAGTGTGTGAGA 57.759 39.130 0.00 0.00 0.00 3.27
600 603 6.248433 ACCCATCAATAAAGTGTGTGAGATT 58.752 36.000 0.00 0.00 0.00 2.40
602 605 7.094205 ACCCATCAATAAAGTGTGTGAGATTTC 60.094 37.037 0.00 0.00 0.00 2.17
603 606 7.121759 CCCATCAATAAAGTGTGTGAGATTTCT 59.878 37.037 0.00 0.00 0.00 2.52
604 607 9.166173 CCATCAATAAAGTGTGTGAGATTTCTA 57.834 33.333 0.00 0.00 0.00 2.10
607 610 9.996554 TCAATAAAGTGTGTGAGATTTCTAAGA 57.003 29.630 0.00 0.00 0.00 2.10
705 711 4.177673 GGACCTACCCTCCTAGCG 57.822 66.667 0.00 0.00 0.00 4.26
731 1873 1.369625 ATGTACTTGCGTTAGCTGCC 58.630 50.000 0.00 0.00 45.42 4.85
1055 3425 3.784338 TCGTAGTTTTTGTGACGGTCTT 58.216 40.909 9.88 0.00 36.02 3.01
1206 3576 2.351060 CCAAGTAGTGACGCGTTCAGTA 60.351 50.000 15.53 16.45 38.88 2.74
1265 3635 5.177142 CAGATTTGGCTCAGATCAATCTACG 59.823 44.000 0.00 0.00 34.85 3.51
1266 3636 2.515926 TGGCTCAGATCAATCTACGC 57.484 50.000 0.00 0.00 34.85 4.42
1442 3814 9.347934 CATATCTTTGCTTACTTACTATCTCCG 57.652 37.037 0.00 0.00 0.00 4.63
1656 4029 6.784969 TGAACCATTTTCCCCTTCTATTTGAA 59.215 34.615 0.00 0.00 0.00 2.69
1737 4420 3.423515 CGTTGTGGAGATTCAACACATCG 60.424 47.826 19.85 19.85 45.56 3.84
1740 4423 2.679837 GTGGAGATTCAACACATCGCAT 59.320 45.455 6.04 0.00 35.30 4.73
1781 4464 5.807011 GCCCACAATGAGATTTGTACATTTC 59.193 40.000 0.00 0.00 37.73 2.17
1893 4576 7.718753 AGAGATCTTGTGTCATCTTCAGTTTTT 59.281 33.333 0.00 0.00 29.01 1.94
2002 4685 1.740296 CCTACCGAGTTTGCACCCG 60.740 63.158 0.00 0.00 0.00 5.28
2339 5035 4.637091 TGTAATGATCTGCATGTTCACCTG 59.363 41.667 0.00 0.00 37.28 4.00
2375 5073 7.857389 CGTATGTATTTGGAAACTGGATGAATG 59.143 37.037 0.00 0.00 0.00 2.67
2400 5098 1.355210 CCGTTTGTTGTTCGCTGCT 59.645 52.632 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.101635 CCCTGTCGTCTCTATGCCGA 61.102 60.000 0.00 0.00 0.00 5.54
26 27 1.360551 CCCTGTCGTCTCTATGCCG 59.639 63.158 0.00 0.00 0.00 5.69
27 28 0.824759 AACCCTGTCGTCTCTATGCC 59.175 55.000 0.00 0.00 0.00 4.40
28 29 2.674796 AAACCCTGTCGTCTCTATGC 57.325 50.000 0.00 0.00 0.00 3.14
29 30 3.491104 GCCTAAACCCTGTCGTCTCTATG 60.491 52.174 0.00 0.00 0.00 2.23
30 31 2.694109 GCCTAAACCCTGTCGTCTCTAT 59.306 50.000 0.00 0.00 0.00 1.98
31 32 2.097825 GCCTAAACCCTGTCGTCTCTA 58.902 52.381 0.00 0.00 0.00 2.43
32 33 0.896226 GCCTAAACCCTGTCGTCTCT 59.104 55.000 0.00 0.00 0.00 3.10
33 34 0.458025 CGCCTAAACCCTGTCGTCTC 60.458 60.000 0.00 0.00 0.00 3.36
34 35 1.590147 CGCCTAAACCCTGTCGTCT 59.410 57.895 0.00 0.00 0.00 4.18
35 36 1.447314 CCGCCTAAACCCTGTCGTC 60.447 63.158 0.00 0.00 0.00 4.20
36 37 2.660802 CCGCCTAAACCCTGTCGT 59.339 61.111 0.00 0.00 0.00 4.34
37 38 2.125269 CCCGCCTAAACCCTGTCG 60.125 66.667 0.00 0.00 0.00 4.35
38 39 2.437895 GCCCGCCTAAACCCTGTC 60.438 66.667 0.00 0.00 0.00 3.51
39 40 4.404098 CGCCCGCCTAAACCCTGT 62.404 66.667 0.00 0.00 0.00 4.00
40 41 4.090588 TCGCCCGCCTAAACCCTG 62.091 66.667 0.00 0.00 0.00 4.45
41 42 4.091939 GTCGCCCGCCTAAACCCT 62.092 66.667 0.00 0.00 0.00 4.34
43 44 4.747529 ACGTCGCCCGCCTAAACC 62.748 66.667 0.00 0.00 41.42 3.27
44 45 3.484547 CACGTCGCCCGCCTAAAC 61.485 66.667 0.00 0.00 41.42 2.01
65 66 4.498520 AGCCACGTCAGCGATCCG 62.499 66.667 1.64 0.00 42.00 4.18
66 67 2.887568 CAGCCACGTCAGCGATCC 60.888 66.667 1.64 0.00 42.00 3.36
67 68 2.279502 TACCAGCCACGTCAGCGATC 62.280 60.000 1.64 0.00 42.00 3.69
68 69 1.676678 ATACCAGCCACGTCAGCGAT 61.677 55.000 1.64 0.00 42.00 4.58
69 70 2.348104 ATACCAGCCACGTCAGCGA 61.348 57.895 1.64 0.00 42.00 4.93
70 71 2.167219 CATACCAGCCACGTCAGCG 61.167 63.158 1.64 0.00 44.93 5.18
71 72 2.464459 GCATACCAGCCACGTCAGC 61.464 63.158 0.00 0.00 0.00 4.26
72 73 3.799753 GCATACCAGCCACGTCAG 58.200 61.111 0.00 0.00 0.00 3.51
94 95 2.100216 CGTATGCAAACGGCTGCC 59.900 61.111 9.11 9.11 45.15 4.85
101 102 1.945207 CGTCCAACACGTATGCAAAC 58.055 50.000 0.00 0.00 44.07 2.93
121 122 4.596180 CATTGATCCGCGGCGCAC 62.596 66.667 32.61 18.93 0.00 5.34
122 123 4.828925 TCATTGATCCGCGGCGCA 62.829 61.111 32.61 18.24 0.00 6.09
123 124 4.299316 GTCATTGATCCGCGGCGC 62.299 66.667 23.51 24.21 0.00 6.53
124 125 3.988385 CGTCATTGATCCGCGGCG 61.988 66.667 23.51 16.78 0.00 6.46
125 126 2.890474 ACGTCATTGATCCGCGGC 60.890 61.111 23.51 8.29 0.00 6.53
126 127 2.525248 CCACGTCATTGATCCGCGG 61.525 63.158 22.12 22.12 0.00 6.46
127 128 3.005898 CCACGTCATTGATCCGCG 58.994 61.111 0.00 0.00 0.00 6.46
128 129 1.439353 ATGCCACGTCATTGATCCGC 61.439 55.000 0.00 0.00 0.00 5.54
129 130 0.305617 CATGCCACGTCATTGATCCG 59.694 55.000 0.00 0.00 0.00 4.18
130 131 0.029834 GCATGCCACGTCATTGATCC 59.970 55.000 6.36 0.00 0.00 3.36
131 132 0.316442 CGCATGCCACGTCATTGATC 60.316 55.000 13.15 0.00 0.00 2.92
132 133 1.717791 CCGCATGCCACGTCATTGAT 61.718 55.000 13.15 0.00 0.00 2.57
133 134 2.397754 CCGCATGCCACGTCATTGA 61.398 57.895 13.15 0.00 0.00 2.57
134 135 2.100797 CCGCATGCCACGTCATTG 59.899 61.111 13.15 0.00 0.00 2.82
135 136 2.046411 TCCGCATGCCACGTCATT 60.046 55.556 13.15 0.00 0.00 2.57
136 137 2.315781 ATCTCCGCATGCCACGTCAT 62.316 55.000 13.15 0.00 0.00 3.06
137 138 1.671901 TATCTCCGCATGCCACGTCA 61.672 55.000 13.15 0.00 0.00 4.35
138 139 0.319900 ATATCTCCGCATGCCACGTC 60.320 55.000 13.15 0.00 0.00 4.34
139 140 0.601046 CATATCTCCGCATGCCACGT 60.601 55.000 13.15 0.00 0.00 4.49
140 141 1.904852 GCATATCTCCGCATGCCACG 61.905 60.000 13.15 0.00 41.36 4.94
141 142 1.871772 GCATATCTCCGCATGCCAC 59.128 57.895 13.15 0.00 41.36 5.01
142 143 4.384599 GCATATCTCCGCATGCCA 57.615 55.556 13.15 0.00 41.36 4.92
144 145 1.374631 TCGGCATATCTCCGCATGC 60.375 57.895 7.91 7.91 46.05 4.06
145 146 1.347097 CGTCGGCATATCTCCGCATG 61.347 60.000 7.82 0.00 46.05 4.06
146 147 1.080501 CGTCGGCATATCTCCGCAT 60.081 57.895 7.82 0.00 46.05 4.73
147 148 2.335011 CGTCGGCATATCTCCGCA 59.665 61.111 7.82 0.00 46.05 5.69
148 149 2.430921 CCGTCGGCATATCTCCGC 60.431 66.667 0.00 3.70 46.05 5.54
166 167 4.586235 GATGGTGGGGATGGGCGG 62.586 72.222 0.00 0.00 0.00 6.13
167 168 4.935495 CGATGGTGGGGATGGGCG 62.935 72.222 0.00 0.00 0.00 6.13
168 169 4.586235 CCGATGGTGGGGATGGGC 62.586 72.222 0.00 0.00 0.00 5.36
169 170 4.586235 GCCGATGGTGGGGATGGG 62.586 72.222 0.00 0.00 0.00 4.00
170 171 1.778017 TATGCCGATGGTGGGGATGG 61.778 60.000 0.00 0.00 36.20 3.51
171 172 0.321919 CTATGCCGATGGTGGGGATG 60.322 60.000 0.00 0.00 36.20 3.51
172 173 0.473694 TCTATGCCGATGGTGGGGAT 60.474 55.000 0.00 0.00 39.17 3.85
173 174 0.473694 ATCTATGCCGATGGTGGGGA 60.474 55.000 0.00 0.00 0.00 4.81
174 175 0.401738 AATCTATGCCGATGGTGGGG 59.598 55.000 0.00 0.00 0.00 4.96
175 176 1.881973 CAAATCTATGCCGATGGTGGG 59.118 52.381 0.00 0.00 0.00 4.61
176 177 2.549754 GTCAAATCTATGCCGATGGTGG 59.450 50.000 0.00 0.00 0.00 4.61
177 178 3.205338 TGTCAAATCTATGCCGATGGTG 58.795 45.455 0.00 0.00 0.00 4.17
178 179 3.558931 TGTCAAATCTATGCCGATGGT 57.441 42.857 0.00 0.00 0.00 3.55
179 180 4.276678 ACATTGTCAAATCTATGCCGATGG 59.723 41.667 0.00 0.00 0.00 3.51
180 181 5.428496 ACATTGTCAAATCTATGCCGATG 57.572 39.130 0.00 0.00 0.00 3.84
181 182 6.293626 GCTAACATTGTCAAATCTATGCCGAT 60.294 38.462 0.00 0.00 0.00 4.18
182 183 5.007626 GCTAACATTGTCAAATCTATGCCGA 59.992 40.000 0.00 0.00 0.00 5.54
183 184 5.207768 GCTAACATTGTCAAATCTATGCCG 58.792 41.667 0.00 0.00 0.00 5.69
184 185 5.523369 GGCTAACATTGTCAAATCTATGCC 58.477 41.667 0.00 0.00 0.00 4.40
185 186 5.007626 TCGGCTAACATTGTCAAATCTATGC 59.992 40.000 0.00 0.00 0.00 3.14
186 187 6.603237 TCGGCTAACATTGTCAAATCTATG 57.397 37.500 0.00 0.00 0.00 2.23
187 188 6.205464 CCATCGGCTAACATTGTCAAATCTAT 59.795 38.462 0.00 0.00 0.00 1.98
188 189 5.527214 CCATCGGCTAACATTGTCAAATCTA 59.473 40.000 0.00 0.00 0.00 1.98
189 190 4.336433 CCATCGGCTAACATTGTCAAATCT 59.664 41.667 0.00 0.00 0.00 2.40
190 191 4.096382 ACCATCGGCTAACATTGTCAAATC 59.904 41.667 0.00 0.00 0.00 2.17
191 192 4.016444 ACCATCGGCTAACATTGTCAAAT 58.984 39.130 0.00 0.00 0.00 2.32
192 193 3.417101 ACCATCGGCTAACATTGTCAAA 58.583 40.909 0.00 0.00 0.00 2.69
193 194 3.006940 GACCATCGGCTAACATTGTCAA 58.993 45.455 0.00 0.00 0.00 3.18
194 195 2.027653 TGACCATCGGCTAACATTGTCA 60.028 45.455 0.00 0.00 0.00 3.58
195 196 2.351726 GTGACCATCGGCTAACATTGTC 59.648 50.000 0.00 0.00 0.00 3.18
196 197 2.356135 GTGACCATCGGCTAACATTGT 58.644 47.619 0.00 0.00 0.00 2.71
197 198 1.327460 CGTGACCATCGGCTAACATTG 59.673 52.381 0.00 0.00 0.00 2.82
198 199 1.651987 CGTGACCATCGGCTAACATT 58.348 50.000 0.00 0.00 0.00 2.71
199 200 0.179084 CCGTGACCATCGGCTAACAT 60.179 55.000 0.00 0.00 41.48 2.71
200 201 1.216977 CCGTGACCATCGGCTAACA 59.783 57.895 0.00 0.00 41.48 2.41
201 202 1.520787 CCCGTGACCATCGGCTAAC 60.521 63.158 0.00 0.00 45.71 2.34
202 203 1.985662 ACCCGTGACCATCGGCTAA 60.986 57.895 0.00 0.00 45.71 3.09
203 204 2.363276 ACCCGTGACCATCGGCTA 60.363 61.111 0.00 0.00 45.71 3.93
204 205 4.082523 CACCCGTGACCATCGGCT 62.083 66.667 0.00 0.00 45.71 5.52
206 207 4.467084 CCCACCCGTGACCATCGG 62.467 72.222 0.00 0.00 46.49 4.18
207 208 3.248446 AACCCACCCGTGACCATCG 62.248 63.158 0.00 0.00 0.00 3.84
208 209 1.376812 GAACCCACCCGTGACCATC 60.377 63.158 0.00 0.00 0.00 3.51
209 210 2.150719 TGAACCCACCCGTGACCAT 61.151 57.895 0.00 0.00 0.00 3.55
210 211 2.768769 TGAACCCACCCGTGACCA 60.769 61.111 0.00 0.00 0.00 4.02
211 212 2.281276 GTGAACCCACCCGTGACC 60.281 66.667 0.00 0.00 37.33 4.02
226 227 4.090588 ATACACGTGGGCCCGGTG 62.091 66.667 32.96 32.96 0.00 4.94
227 228 4.090588 CATACACGTGGGCCCGGT 62.091 66.667 21.57 15.49 0.00 5.28
231 232 4.460683 TCGGCATACACGTGGGCC 62.461 66.667 27.95 27.95 42.98 5.80
232 233 3.192922 GTCGGCATACACGTGGGC 61.193 66.667 21.57 19.15 0.00 5.36
233 234 2.883730 CGTCGGCATACACGTGGG 60.884 66.667 21.57 10.08 0.00 4.61
234 235 2.156446 GTCGTCGGCATACACGTGG 61.156 63.158 21.57 2.89 37.30 4.94
235 236 0.097499 TAGTCGTCGGCATACACGTG 59.903 55.000 15.48 15.48 37.30 4.49
236 237 0.376152 CTAGTCGTCGGCATACACGT 59.624 55.000 0.00 0.00 37.30 4.49
237 238 0.376152 ACTAGTCGTCGGCATACACG 59.624 55.000 0.00 0.00 37.36 4.49
238 239 2.556534 AACTAGTCGTCGGCATACAC 57.443 50.000 0.00 0.00 0.00 2.90
239 240 4.603985 CATAAACTAGTCGTCGGCATACA 58.396 43.478 0.00 0.00 0.00 2.29
240 241 3.424529 GCATAAACTAGTCGTCGGCATAC 59.575 47.826 0.00 0.00 0.00 2.39
241 242 3.551454 GGCATAAACTAGTCGTCGGCATA 60.551 47.826 0.00 0.00 0.00 3.14
242 243 2.470821 GCATAAACTAGTCGTCGGCAT 58.529 47.619 0.00 0.00 0.00 4.40
243 244 1.470285 GGCATAAACTAGTCGTCGGCA 60.470 52.381 0.00 0.00 0.00 5.69
244 245 1.206523 GGCATAAACTAGTCGTCGGC 58.793 55.000 0.00 0.00 0.00 5.54
245 246 1.064505 TCGGCATAAACTAGTCGTCGG 59.935 52.381 0.00 0.00 0.00 4.79
246 247 2.107178 GTCGGCATAAACTAGTCGTCG 58.893 52.381 0.00 0.00 0.00 5.12
247 248 2.107178 CGTCGGCATAAACTAGTCGTC 58.893 52.381 0.00 0.00 0.00 4.20
248 249 1.202222 CCGTCGGCATAAACTAGTCGT 60.202 52.381 0.00 0.00 0.00 4.34
249 250 1.474017 CCGTCGGCATAAACTAGTCG 58.526 55.000 0.00 0.00 0.00 4.18
268 269 4.077188 GAACACGCCGACAGCTGC 62.077 66.667 15.27 5.81 40.39 5.25
269 270 2.356313 AGAACACGCCGACAGCTG 60.356 61.111 13.48 13.48 40.39 4.24
270 271 2.049063 GAGAACACGCCGACAGCT 60.049 61.111 0.00 0.00 40.39 4.24
271 272 2.355837 TGAGAACACGCCGACAGC 60.356 61.111 0.00 0.00 38.52 4.40
272 273 2.375766 GCTGAGAACACGCCGACAG 61.376 63.158 0.00 0.00 0.00 3.51
273 274 1.520600 TAGCTGAGAACACGCCGACA 61.521 55.000 0.00 0.00 0.00 4.35
274 275 0.798771 CTAGCTGAGAACACGCCGAC 60.799 60.000 0.00 0.00 0.00 4.79
275 276 1.506718 CTAGCTGAGAACACGCCGA 59.493 57.895 0.00 0.00 0.00 5.54
276 277 1.517257 CCTAGCTGAGAACACGCCG 60.517 63.158 0.00 0.00 0.00 6.46
277 278 1.811679 GCCTAGCTGAGAACACGCC 60.812 63.158 0.00 0.00 0.00 5.68
278 279 1.811679 GGCCTAGCTGAGAACACGC 60.812 63.158 0.00 0.00 0.00 5.34
279 280 1.517257 CGGCCTAGCTGAGAACACG 60.517 63.158 0.00 0.00 37.02 4.49
280 281 1.153549 CCGGCCTAGCTGAGAACAC 60.154 63.158 0.00 0.00 37.02 3.32
281 282 3.019003 GCCGGCCTAGCTGAGAACA 62.019 63.158 18.11 0.00 37.02 3.18
282 283 2.202946 GCCGGCCTAGCTGAGAAC 60.203 66.667 18.11 0.00 37.02 3.01
283 284 3.838271 CGCCGGCCTAGCTGAGAA 61.838 66.667 23.46 0.00 37.02 2.87
295 296 2.102161 GCACAAAATAGCCGCCGG 59.898 61.111 0.00 0.00 0.00 6.13
296 297 2.102161 GGCACAAAATAGCCGCCG 59.898 61.111 0.00 0.00 41.70 6.46
301 302 0.519961 AACCGTCGGCACAAAATAGC 59.480 50.000 12.28 0.00 0.00 2.97
302 303 1.727857 GCAACCGTCGGCACAAAATAG 60.728 52.381 12.28 0.00 0.00 1.73
303 304 0.238817 GCAACCGTCGGCACAAAATA 59.761 50.000 12.28 0.00 0.00 1.40
304 305 1.007849 GCAACCGTCGGCACAAAAT 60.008 52.632 12.28 0.00 0.00 1.82
305 306 2.409651 GCAACCGTCGGCACAAAA 59.590 55.556 12.28 0.00 0.00 2.44
306 307 3.587933 GGCAACCGTCGGCACAAA 61.588 61.111 12.28 0.00 0.00 2.83
327 328 1.740905 GGCTACTCCGGTCTAAGCC 59.259 63.158 19.01 19.01 45.37 4.35
328 329 1.740905 GGGCTACTCCGGTCTAAGC 59.259 63.158 0.00 6.82 34.94 3.09
329 330 2.031360 CGGGCTACTCCGGTCTAAG 58.969 63.158 0.00 0.00 45.78 2.18
330 331 4.247781 CGGGCTACTCCGGTCTAA 57.752 61.111 0.00 0.00 45.78 2.10
344 345 4.838152 CACATCCTGGCCGTCGGG 62.838 72.222 14.38 0.00 43.43 5.14
345 346 4.838152 CCACATCCTGGCCGTCGG 62.838 72.222 6.99 6.99 31.36 4.79
352 353 2.821366 GCGACAGCCACATCCTGG 60.821 66.667 0.00 0.00 44.08 4.45
365 366 3.570559 GTCTAGATTGAGCTATGGCGAC 58.429 50.000 0.00 0.00 44.37 5.19
366 367 2.558795 GGTCTAGATTGAGCTATGGCGA 59.441 50.000 0.00 0.00 44.37 5.54
367 368 2.669670 CGGTCTAGATTGAGCTATGGCG 60.670 54.545 0.00 0.00 44.37 5.69
368 369 2.558795 TCGGTCTAGATTGAGCTATGGC 59.441 50.000 0.00 0.00 39.06 4.40
369 370 3.365465 CGTCGGTCTAGATTGAGCTATGG 60.365 52.174 0.00 0.00 32.83 2.74
370 371 3.365465 CCGTCGGTCTAGATTGAGCTATG 60.365 52.174 2.08 0.00 32.83 2.23
371 372 2.814919 CCGTCGGTCTAGATTGAGCTAT 59.185 50.000 2.08 0.00 32.83 2.97
372 373 2.219458 CCGTCGGTCTAGATTGAGCTA 58.781 52.381 2.08 0.00 32.83 3.32
373 374 1.025812 CCGTCGGTCTAGATTGAGCT 58.974 55.000 2.08 0.00 32.83 4.09
374 375 0.595310 GCCGTCGGTCTAGATTGAGC 60.595 60.000 13.94 0.00 0.00 4.26
375 376 0.317103 CGCCGTCGGTCTAGATTGAG 60.317 60.000 13.94 0.00 0.00 3.02
376 377 1.725665 CGCCGTCGGTCTAGATTGA 59.274 57.895 13.94 0.00 0.00 2.57
377 378 4.303853 CGCCGTCGGTCTAGATTG 57.696 61.111 13.94 0.00 0.00 2.67
392 393 2.747507 AAAACAATGCTGACGGCCGC 62.748 55.000 28.58 19.01 40.92 6.53
393 394 1.003262 CAAAACAATGCTGACGGCCG 61.003 55.000 26.86 26.86 40.92 6.13
394 395 0.667184 CCAAAACAATGCTGACGGCC 60.667 55.000 3.22 0.00 40.92 6.13
395 396 1.284297 GCCAAAACAATGCTGACGGC 61.284 55.000 0.00 0.00 42.22 5.68
396 397 0.667184 GGCCAAAACAATGCTGACGG 60.667 55.000 0.00 0.00 0.00 4.79
397 398 1.003262 CGGCCAAAACAATGCTGACG 61.003 55.000 2.24 0.00 33.12 4.35
398 399 0.031994 ACGGCCAAAACAATGCTGAC 59.968 50.000 2.24 0.00 35.37 3.51
399 400 0.313672 GACGGCCAAAACAATGCTGA 59.686 50.000 2.24 0.00 35.37 4.26
400 401 1.003262 CGACGGCCAAAACAATGCTG 61.003 55.000 2.24 0.00 37.40 4.41
401 402 1.285641 CGACGGCCAAAACAATGCT 59.714 52.632 2.24 0.00 0.00 3.79
402 403 1.732683 CCGACGGCCAAAACAATGC 60.733 57.895 2.24 0.00 0.00 3.56
403 404 1.080839 CCCGACGGCCAAAACAATG 60.081 57.895 8.86 0.00 0.00 2.82
404 405 2.272447 CCCCGACGGCCAAAACAAT 61.272 57.895 8.86 0.00 0.00 2.71
405 406 2.335092 TACCCCGACGGCCAAAACAA 62.335 55.000 8.86 0.00 33.26 2.83
406 407 2.734948 CTACCCCGACGGCCAAAACA 62.735 60.000 8.86 0.00 33.26 2.83
407 408 2.032376 TACCCCGACGGCCAAAAC 59.968 61.111 8.86 0.00 33.26 2.43
408 409 2.348243 CTACCCCGACGGCCAAAA 59.652 61.111 8.86 0.00 33.26 2.44
409 410 3.708544 CCTACCCCGACGGCCAAA 61.709 66.667 8.86 0.00 33.26 3.28
410 411 4.700448 TCCTACCCCGACGGCCAA 62.700 66.667 8.86 0.00 33.26 4.52
413 414 3.525545 GAGTCCTACCCCGACGGC 61.526 72.222 8.86 0.00 35.33 5.68
414 415 0.969409 AAAGAGTCCTACCCCGACGG 60.969 60.000 6.99 6.99 35.33 4.79
415 416 0.893447 AAAAGAGTCCTACCCCGACG 59.107 55.000 0.00 0.00 35.33 5.12
416 417 2.094130 CAGAAAAGAGTCCTACCCCGAC 60.094 54.545 0.00 0.00 0.00 4.79
417 418 2.176889 CAGAAAAGAGTCCTACCCCGA 58.823 52.381 0.00 0.00 0.00 5.14
418 419 1.207329 CCAGAAAAGAGTCCTACCCCG 59.793 57.143 0.00 0.00 0.00 5.73
419 420 2.267192 ACCAGAAAAGAGTCCTACCCC 58.733 52.381 0.00 0.00 0.00 4.95
420 421 4.081586 CACTACCAGAAAAGAGTCCTACCC 60.082 50.000 0.00 0.00 0.00 3.69
421 422 4.081586 CCACTACCAGAAAAGAGTCCTACC 60.082 50.000 0.00 0.00 0.00 3.18
422 423 4.081586 CCCACTACCAGAAAAGAGTCCTAC 60.082 50.000 0.00 0.00 0.00 3.18
423 424 4.094476 CCCACTACCAGAAAAGAGTCCTA 58.906 47.826 0.00 0.00 0.00 2.94
424 425 2.907042 CCCACTACCAGAAAAGAGTCCT 59.093 50.000 0.00 0.00 0.00 3.85
425 426 2.615747 GCCCACTACCAGAAAAGAGTCC 60.616 54.545 0.00 0.00 0.00 3.85
426 427 2.701107 GCCCACTACCAGAAAAGAGTC 58.299 52.381 0.00 0.00 0.00 3.36
427 428 1.002087 CGCCCACTACCAGAAAAGAGT 59.998 52.381 0.00 0.00 0.00 3.24
428 429 1.002087 ACGCCCACTACCAGAAAAGAG 59.998 52.381 0.00 0.00 0.00 2.85
429 430 1.053424 ACGCCCACTACCAGAAAAGA 58.947 50.000 0.00 0.00 0.00 2.52
430 431 2.618053 CTACGCCCACTACCAGAAAAG 58.382 52.381 0.00 0.00 0.00 2.27
431 432 1.338389 GCTACGCCCACTACCAGAAAA 60.338 52.381 0.00 0.00 0.00 2.29
432 433 0.248289 GCTACGCCCACTACCAGAAA 59.752 55.000 0.00 0.00 0.00 2.52
433 434 0.901114 TGCTACGCCCACTACCAGAA 60.901 55.000 0.00 0.00 0.00 3.02
434 435 1.304630 TGCTACGCCCACTACCAGA 60.305 57.895 0.00 0.00 0.00 3.86
435 436 1.141881 CTGCTACGCCCACTACCAG 59.858 63.158 0.00 0.00 0.00 4.00
436 437 0.901114 TTCTGCTACGCCCACTACCA 60.901 55.000 0.00 0.00 0.00 3.25
437 438 0.179108 CTTCTGCTACGCCCACTACC 60.179 60.000 0.00 0.00 0.00 3.18
438 439 0.815734 TCTTCTGCTACGCCCACTAC 59.184 55.000 0.00 0.00 0.00 2.73
439 440 1.552578 TTCTTCTGCTACGCCCACTA 58.447 50.000 0.00 0.00 0.00 2.74
440 441 0.905357 ATTCTTCTGCTACGCCCACT 59.095 50.000 0.00 0.00 0.00 4.00
441 442 1.291132 GATTCTTCTGCTACGCCCAC 58.709 55.000 0.00 0.00 0.00 4.61
442 443 0.178068 GGATTCTTCTGCTACGCCCA 59.822 55.000 0.00 0.00 0.00 5.36
443 444 0.178068 TGGATTCTTCTGCTACGCCC 59.822 55.000 0.00 0.00 0.00 6.13
444 445 1.137086 TCTGGATTCTTCTGCTACGCC 59.863 52.381 0.00 0.00 0.00 5.68
445 446 2.197577 GTCTGGATTCTTCTGCTACGC 58.802 52.381 0.00 0.00 0.00 4.42
446 447 3.443037 CTGTCTGGATTCTTCTGCTACG 58.557 50.000 0.00 0.00 0.00 3.51
447 448 3.431486 CCCTGTCTGGATTCTTCTGCTAC 60.431 52.174 0.00 0.00 38.35 3.58
457 458 1.277580 CCTCAGGCCCTGTCTGGATT 61.278 60.000 11.27 0.00 35.77 3.01
459 460 2.284921 CCTCAGGCCCTGTCTGGA 60.285 66.667 11.27 0.00 35.77 3.86
488 489 2.686835 GCTCTGACCCTGGCCTCT 60.687 66.667 3.32 0.00 0.00 3.69
495 496 2.686835 GCCCTCTGCTCTGACCCT 60.687 66.667 0.00 0.00 36.87 4.34
731 1873 9.087424 TCTCGATGTGTTGTCATTAATTTAGAG 57.913 33.333 0.00 0.00 0.00 2.43
1063 3433 3.168035 ACTTGCCCATGTATGGTTTGA 57.832 42.857 9.87 0.00 46.65 2.69
1206 3576 1.422531 TGCAAATTGCCAGGAGGTTT 58.577 45.000 15.98 0.00 44.23 3.27
1489 3861 6.738453 GCCCAACTCAAAAGTGAACAATGTAT 60.738 38.462 0.00 0.00 35.36 2.29
1656 4029 5.865085 TGGTGAGTAACTAGATTTGCAAGT 58.135 37.500 0.00 0.00 0.00 3.16
1711 4394 1.069227 GTTGAATCTCCACAACGTGCC 60.069 52.381 0.00 0.00 37.29 5.01
1715 4398 3.423515 CGATGTGTTGAATCTCCACAACG 60.424 47.826 15.83 15.83 46.06 4.10
1737 4420 3.058639 GGCTATCGTCTTTGAATGGATGC 60.059 47.826 0.00 0.00 0.00 3.91
1740 4423 2.503765 TGGGCTATCGTCTTTGAATGGA 59.496 45.455 0.00 0.00 0.00 3.41
1893 4576 5.743130 GCATCGGAGATTAAAATCCCTCTCA 60.743 44.000 4.40 0.00 45.12 3.27
1976 4659 2.422597 CAAACTCGGTAGGCAATCACA 58.577 47.619 0.00 0.00 0.00 3.58
2179 4865 6.073765 ACAACTAGTACATGAAAGCAAACGAG 60.074 38.462 0.00 0.00 0.00 4.18
2304 5000 8.750515 TGCAGATCATTACAGGAAATAAATCA 57.249 30.769 0.00 0.00 0.00 2.57
2305 5001 9.622004 CATGCAGATCATTACAGGAAATAAATC 57.378 33.333 0.00 0.00 31.79 2.17
2339 5035 6.671614 TCCAAATACATACGAATGTGGTTC 57.328 37.500 1.34 0.00 45.99 3.62
2375 5073 1.525619 CGAACAACAAACGGGAGAGTC 59.474 52.381 0.00 0.00 0.00 3.36
2400 5098 4.097741 AGTTACTTCACAACTTGCATTGCA 59.902 37.500 7.38 7.38 32.28 4.08
2475 5188 5.333111 GGTGAACTTTAGTCTTAACTGTGCG 60.333 44.000 0.00 0.00 36.92 5.34


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.